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Frontiers in Medicine 2022To determine whether gut microbiota, fatty metabolism and cytokines were associated with immune thrombocytopenia (ITP).
OBJECTIVE
To determine whether gut microbiota, fatty metabolism and cytokines were associated with immune thrombocytopenia (ITP).
METHODS
In total, 29 preliminarily diagnosed ITP patients and 33 healthy volunteers were enrolled. Fecal bacterial were analyzed based on 16S rRNA sequencing. Plasma cytokines and motabolites were analyzed using flow cytometry and liquid chromatography-mass spectrometry (LC-MS), respectively.
RESULTS
, , and were enriched at the genus level in ITP patients, while , , were depleted. At the phylum level, the relative abundance of and increased in ITP patients, while , , and the ratio decreased. Plasma levels of 5-hydroxyeicosatetraenoic acid (5-HETE), 6-trans-12-epi-leukotriene B4 (6t,12e-LTB), and resolvin D2 (RvD) were upregulated, and stachydrine, dowicide A, dodecanoylcarnitine were downregulated in ITP patients. Furthermore, RvD is positively correlated with order , 5-HETE is positively correlated with genus , and 6t,12e-LTB is positively correlated with genus . In addition, stachydrine is positively correlated with family , dowicide A is positively correlated with class , and dodecanoylcarnitine is positively correlated with order . Plasma levels of interleukin-6 (IL-6) and tumor necrosis factor-α (TNF-α) were upregulated in ITP patients.
CONCLUSION
Our study revealed a relationship between microbiota and fatty metabolism in ITP. Gut microbiota may participate in the pathogenesis of ITP through affecting cytokine secretion, interfering with fatty metabolism.
PubMed: 35665326
DOI: 10.3389/fmed.2022.810612 -
Frontiers in Microbiology 2022Malic acid is a component of the rhizosphere exudate and is vital for crop growth. However, little information is available about the effects of external applications of...
Malic acid is a component of the rhizosphere exudate and is vital for crop growth. However, little information is available about the effects of external applications of malic acid on the nutrient absorption and quality of grape fruit, and few studies have been performed on the relationship between the changes in the rhizosphere microbial community and nutrient absorption and fruit quality of grapes after adding malic acid. Here, the LM (low concentration of malic acid) and HM (high concentration of malic acid) treatments comprised 5% and 10% malic acid (the ratio of acid to the total weight of the fertilizer) combined with NPK fertilizer, respectively. Applying malic acid changed the grape rhizosphere microbial community structure and community-level physiological profile (CLPP) significantly, and HM had a positive effect on the utilization of substrates. The microbial community structure in the rhizosphere of the grapes with added malic acid was closely related to the CLPP. The N and P content in the leaves and fruits increased after applying malic acid compared to the control, while K content in the fruits increased significantly. In addition, malic acid significantly reduced the weight per fruit, significantly increased soluble sugar content (SSC) and vitamin C content of the fruit, and significantly improved the fruit sugar-acid ratio and grape tasting score. Moreover, the principal component analysis and grape nutrient and fruit quality scores showed that grape nutrients and fruit quality were significantly affected by malic acid and ranked as 5% malic acid > 10% malic acid > control. Pearson's correlation heatmap of microbial composition, nutrient absorption and fruit quality of the grapes showed that the grape microbial community was closely related to grape nutrients and fruit quality. Adding malic acid was positively correlated to , , and . Furthermore, , , and were closely related to grape nutrient absorption and fruit quality. and were positively correlated with total soluble sugar, while and were positively correlated with titratable acid. Hence, and were the key bacteria that played a major role in grape fruit quality and nutrient absorption after applying malic acid water-soluble fertilizer.
PubMed: 35663858
DOI: 10.3389/fmicb.2022.850807 -
Journal of Bacteriology Jun 2022The current classification of the phylum (new name, ) features eight distinct classes, six of which include known spore-forming bacteria. In Bacillus subtilis,...
The current classification of the phylum (new name, ) features eight distinct classes, six of which include known spore-forming bacteria. In Bacillus subtilis, sporulation involves up to 500 genes, many of which do not have orthologs in other bacilli and/or clostridia. Previous studies identified about 60 sporulation genes of B. subtilis that were shared by all spore-forming members of the . These genes are referred to as the sporulation core or signature, although many of these are also found in genomes of nonsporeformers. Using an expanded set of 180 firmicute genomes from 160 genera, including 76 spore-forming species, we investigated the conservation of the sporulation genes, in particular seeking to identify lineages that lack some of the genes from the conserved sporulation core. The results of this analysis confirmed that many small acid-soluble spore proteins (SASPs), spore coat proteins, and germination proteins, which were previously characterized in bacilli, are missing in spore-forming members of and other classes of . A particularly dramatic loss of sporulation genes was observed in the spore-forming members of the families and . Fifteen species from diverse lineages were found to carry (-interrupting) elements of different sizes that all encoded SpoIVCA-like recombinases but did not share any other genes. Phylogenetic trees built from concatenated alignments of sporulation proteins and ribosomal proteins showed similar topology, indicating an early origin and subsequent vertical inheritance of the sporulation genes. Many members of the phylum () are capable of producing endospores, which enhance the survival of important Gram-positive pathogens that cause such diseases as anthrax, botulism, colitis, gas gangrene, and tetanus. We show that the core set of sporulation genes, defined previously through genome comparisons of several bacilli and clostridia, is conserved in a wide variety of sporeformers from several distinct lineages of . We also detected widespread loss of sporulation genes in many organisms, particularly within the families and Members of these families, such as Lysinibacillus sphaericus and Clostridium innocuum, could be excellent model organisms for studying sporulation mechanisms, such as engulfment, formation of the spore coat, and spore germination.
Topics: Bacillus; Bacillus subtilis; Bacterial Proteins; Clostridium; Firmicutes; Humans; Phylogeny; Spores, Bacterial
PubMed: 35638784
DOI: 10.1128/jb.00079-22 -
Biomolecules Feb 2022Prokaryotic Argonautes (pAgos) from mesophilic bacteria are attracting increasing attention for their genome editing potential. So far, it has been reported that KmAgo...
Prokaryotic Argonautes (pAgos) from mesophilic bacteria are attracting increasing attention for their genome editing potential. So far, it has been reported that KmAgo from can utilize DNA and RNA guide of any sequence to effectively cleave DNA and RNA targets. Here we find that three active pAgos, which have about 50% sequence identity with KmAgo, possess typical DNA-guided DNA target cleavage ability. Among them, RsuAgo from is mainly explored for which can cleave both DNA and RNA targets. Interestingly, RsuAgo-mediated RNA target cleavage occurs only with short guide DNAs in a narrow length range (16-20 nt), and mismatches between the guide and target sequence greatly affect the efficiency of RNA target cleavage. RsuAgo-mediated target cleavage shows a preference for a guide strand with a 5'-terminal A residue. Furthermore, we have found that RsuAgo can cleave double-stranded DNA in a low-salt buffer at 37 °C. These properties of RsuAgo provide a new tool for DNA and RNA manipulation at moderate temperatures.
Topics: Argonaute Proteins; Bacteria; Bacterial Proteins; DNA; Endonucleases; Planococcaceae; RNA
PubMed: 35327547
DOI: 10.3390/biom12030355 -
Microbial Cell Factories Mar 2022The genus Planococcus is comprised of halophilic bacteria generally reported for the production of carotenoid pigments and biosurfactants. In previous work, we showed...
BACKGROUND
The genus Planococcus is comprised of halophilic bacteria generally reported for the production of carotenoid pigments and biosurfactants. In previous work, we showed that the culturing of the orange-pigmented Planococcus sp. CP5-4 isolate increased the evaporation rate of industrial wastewater brine effluent, which we attributed to the orange pigment. This demonstrated the potential application of this bacterium for industrial brine effluent management in evaporation ponds for inland desalination plants. Here we identified a C-carotenoid biosynthetic gene cluster responsible for pigment biosynthesis in Planococcus sp. CP5-4 through isolation of mutants and genome sequencing. We further compare the core genes of the carotenoid biosynthetic gene clusters identified from different Planococcus species' genomes which grouped into gene cluster families containing BGCs linked to different carotenoid product chemotypes. Lastly, LC-MS analysis of saponified and unsaponified pigment extracts obtained from cultures of Planococcus sp. CP5-4, revealed the structure of the main (predominant) glucosylated C-carotenoid fatty acid ester produced by Planococcus sp. CP5-4.
RESULTS
Genome sequence comparisons of isolated mutant strains of Planococcus sp. CP5-4 showed deletions of 146 Kb and 3 Kb for the non-pigmented and "yellow" mutants respectively. Eight candidate genes, likely responsible for C-carotenoid biosynthesis, were identified on the wild-type genome region corresponding to the deleted segment in the non-pigmented mutant. Six of the eight candidate genes formed a biosynthetic gene cluster. A truncation of crtP was responsible for the "yellow" mutant phenotype. Genome annotation revealed that the genes encoded 4,4'-diapolycopene oxygenase (CrtNb), 4,4'- diapolycopen-4-al dehydrogenase (CrtNc), 4,4'-diapophytoene desaturase (CrtN), 4,4'- diaponeurosporene oxygenase (CrtP), glycerol acyltransferase (Agpat), family 2 glucosyl transferase 2 (Gtf2), phytoene/squalene synthase (CrtM), and cytochrome P450 hydroxylase enzymes. Carotenoid analysis showed that a glucosylated C-carotenoid fatty acid ester, methyl 5-(6-C)-glucosyl-5, 6'-dihydro-apo-4, 4'-lycopenoate was the main carotenoid compound produced by Planococcus sp. CP5-4.
CONCLUSION
We identified and characterized the carotenoid biosynthetic gene cluster and the C-carotenoid compound produced by Planococcus sp. CP5-4. Mass-spectrometry guided analysis of the saponified and unsaponified pigment extracts showed that methyl 5-glucosyl-5, 6-dihydro-apo-4, 4'-lycopenoate esterified to heptadecatrienoic acid (C). Furthermore, through phylogenetic analysis of the core carotenoid BGCs of Planococcus species we show that various C-carotenoid product chemotypes, apart from methyl 5-glucosyl-5, 6-dihydro-apo-4, 4'-lycopenoate and 5-glucosyl-4, 4-diaponeurosporen-4'-ol-4-oic acid, may be produced that could offer opportunities for a variety of applications.
Topics: Carotenoids; Multigene Family; Phylogeny; Planococcus Bacteria; South Africa
PubMed: 35305628
DOI: 10.1186/s12934-022-01752-1 -
Journal of Animal Science and... Jan 2022Previous studies had shown that short-term acute heat stress (HS) affected the host's metabolism and intestinal microbiota independent of feed intake (FI) reduction, and...
Alterations in intestinal microbiota composition coincide with impaired intestinal morphology and dysfunctional ileal immune response in growing-finishing pigs under constant chronic heat stress.
BACKGROUND
Previous studies had shown that short-term acute heat stress (HS) affected the host's metabolism and intestinal microbiota independent of feed intake (FI) reduction, and long-term calorie restriction caused intestinal morphological injuries and gut microbial alterations. However, research on the effects of constant chronic HS on intestinal microbial composition and the roles of FI reduction played in is limited. This study aimed to investigate the effects of 7-day constant chronic HS on the composition of intestinal microbes in growing-finishing pigs, and its relationship with pigs' performance, intestinal morphology, and ileal immune response. Twenty-four growing-finishing pigs (Duroc × Large White × Landrace, 30 ± 1 kg body weight) were randomly assigned to three treatments (n = 8), 1) thermal neutral (TN) conditions (25 ± 1 °C) with ad libitum FI, 2) HS conditions (35 ± 1 °C) with ad libitum FI, 3) pair-fed (PF) with HS under TN conditions to discriminate the confounding effects of dissimilar FI, and the FI was the previous day's average FI of HS. The small intestinal segments (duodenum, jejunum, and ileum) and feces were collected on d 8.
RESULTS
Results indicated that HS drastically declined (P < 0.05) average daily gain (ADG) and average daily feed intake (ADFI) (about 61%) in comparison with TN, and caused hyperpyrexia, meanwhile PF caused hypothermia. Morphological observation by light and electron microscopes showed that both HS and PF treatment decreased (P < 0.05) the villus and microvillus height compared with TN. Additionally, HS increased (P < 0.05) protein expression of heat shock protein 70 in the duodenum, jejunum, and ileum. Furthermore, the expression of tight junction protein zonula occluden-1 (ZO-1) in the duodenum and ileum, and Occludin in the ileum were enhanced (P < 0.05) compared with TN and PF. Moreover, HS significantly enhanced (P < 0.05) the mRNA relative expression of inflammatory cytokines (TLR-2, TLR-4, and tumor necrosis factor-α (TNF-α), IL-6, IL-8, PG1-5, β-defensin 2 (pBD-2)), mucins (mucin-1 and mucin-2) and P65 protein level in the ileal mucosa tissue. Intestinal microbiota analysis by 16S rRNA sequencing showed lower (P < 0.10) α diversity in both HS and PF, and a separated cluster of β diversity among groups. Compared with TN, HS but not PF mainly reduced (FDR < 0.05) Bacteroidetes (phylum), Bacteroidia (class) and elevated the proportions of Proteobacteria (phylum, FDR < 0.05), Bacillales (order, FDR < 0.05), Planococcaceae (family, FDR < 0.05), Kurthia (genus, FDR < 0.05), Streptococcaceae (family, FDR < 0.10) and Streptococcus (genus, FDR < 0.10). Notably, Lactobacillales (order) was decreased (FDR < 0.05) by PF alone. Furthermore, the Spearman correlation analysis indicated that the microbes prevalent in HS were positively (P < 0.05) associated with intestinal morphological injuries indicators and ileal immune response parameters, and the microbes reduced in HS were negatively (P < 0.05) with the performance data.
CONCLUSIONS
Intestinal morphological injuries and ileal immune response caused by constant chronic HS independent of FI showed close connections with alterations in intestinal microbiota in growing-finishing pigs.
PubMed: 34983683
DOI: 10.1186/s40104-021-00651-6 -
Heliyon Oct 2021Microorganisms in clay barriers could affect the long-term performance of waste containers in future deep geological repositories (DGR) for used nuclear fuel through...
Microorganisms in clay barriers could affect the long-term performance of waste containers in future deep geological repositories (DGR) for used nuclear fuel through production of corrosive metabolites ( sulfide), which is why clay materials are highly compacted: to reduce both physical space and access to water for microorganisms to grow. However, the highly compacted nature of clays and the resulting low activity or dormancy of microorganisms complicate the extraction of biomarkers ( PLFA, DNA .) from such barriers for predictive analysis of microbial risks. In order to overcome these challenges, we have combined culture- and 16S rRNA gene amplicon sequencing-based approaches to describe the functional diversity of microorganisms in several commercial clay products, including two different samples of Wyoming type MX-80 bentonite (Batch 1 and Batch 2), the reference clay for a future Canadian DGR, and Avonlea type Canaprill, a clay sample for comparison. Microorganisms from bentonites were enriched in anoxic 10% w/v clay microcosms for three months at ambient temperature with addition of 10% hydrogen along with presumable indigenous organics and sulfate in the clay. High-throughput sequencing of 16S rRNA gene fragments indicated a high abundance of Gram-positive bacteria of the phylum Firmicutes (82%) in MX-80 Batch 1 incubations. Bacterial libraries from microcosms with MX-80 Batch 2 were enriched with Firmicutes (53%) and Chloroflexi (43%). Firmicutes also significantly contributed (<15%) to the bacterial community in Canaprill clay microcosm, which was dominated by Gram-negative Proteobacteria (>70%). Sequence analysis revealed presence of the bacterial families and in MX-80 Batch 1 incubations; along with unidentified bacteria of the phylum Chloroflexi, in MX-80 Batch 2 clay microcosms, and in Canaprill microcosms. Exploration of potential metabolic pathways in the bacterial communities from the clay microcosms suggested variable patterns of sulfur cycling in the different clays with the possible prevalence of bacterial sulfate-reduction in MX-80 bentonite, and probably successive sulfate-reduction/sulfur-oxidation reactions in Canaprill microcosms. Furthermore, analysis of potential metabolic pathways in the bentonite enrichments suggested that bacteria with acid-producing capabilities (, fermenters and acetogens) together with sulfide-producing prokaryotes might perhaps contribute to corrosion risks in clay systems. However, the low activity or dormancy of microorganisms in highly compacted bentonites as a result of severe environmental constraints ( low water activity and high swelling pressure in the confined bentonite) would be expected to largely inhibit bacterial activity in highly compacted clay-based barriers in a future DGR.
PubMed: 34703919
DOI: 10.1016/j.heliyon.2021.e08131 -
BMC Microbiology Oct 2021Extremophiles have attracted much attention in the last few decades, as they possess different properties by producing certain useful metabolites. However, the secondary...
BACKGROUND
Extremophiles have attracted much attention in the last few decades, as they possess different properties by producing certain useful metabolites. However, the secondary metabolism of the extremophiles of Antarctic krill has received little attention.
RESULTS
In this study, a new bacterial strain MSAK28401 from Antarctic krill was isolated and identified. The results of analysis on phenotypic, chemotaxonomic, and genomic characteristics showed that the strain MSAK28401 belongs to the genus Planococcus. Cells of this strain were coccoid (0.89-1.05 μm) and aerobic. The majority of the fatty acid content was C anteiso (37.67 ± 0.90%) followed by C ω7c alcohol (10.37 ± 1.22%) and C iso (9.36 ± 0.71%). The calculated average nucleotide identity and DNA-DNA hybridization values between the strain MSAK28401 and type strains P. citreus DSM 20549 and P. rifietoensis M8 were lower than 91 and 70%, respectively. The strain MSAK28401 (=KCTC 43283 and MCCC 1k05448) represented a new member of the genus Planococcus and was named P. alpniumensis sp. nov. Moreover, genes involved in the degradation of aromatic compounds (e.g., salicylate, gentisate, and quinate) were found in the genome, implying that strain MSAK28401 has an aromatic compound as its potential metabolite. This work will help us understand the genomic characteristics and potential metabolic pathway of Planococcus from Antarctic krill.
CONCLUSIONS
This study reported the genomic information and phenotypic characteristics of the new strain P. alpniumensis MSAK28401 isolated from Antarctic krill, and provided the genome information of Planococcus strains for further studying the function roles in aromatic compound metabolism.
Topics: Animals; Antarctic Regions; Bacterial Proteins; DNA, Bacterial; Euphausiacea; Extremophiles; Fatty Acids; Genome, Bacterial; Nucleic Acid Hybridization; Phenotype; Phylogeny; Planococcus Bacteria; Secondary Metabolism; Sequence Analysis, DNA
PubMed: 34686131
DOI: 10.1186/s12866-021-02347-3 -
Molecules (Basel, Switzerland) Oct 2021The use of additives has generated significant attention due to their extensive application in the microbially induced calcium carbonate precipitation (MICP) process....
The use of additives has generated significant attention due to their extensive application in the microbially induced calcium carbonate precipitation (MICP) process. This study aims to discuss the effects of Na-montmorillonite (Na-MMT) on CaCO crystallization and sandy soil consolidation through the MICP process. Compared with the traditional MICP method, a larger amount of CaCO precipitate was obtained. Moreover, the reaction of Ca ions was accelerated, and bacteria were absorbed by a small amount of Na-MMT. Meanwhile, an increase in the total cementing solution (TCS) was not conducive to the previous reaction. This problem was solved by conducting the reaction with Na-MMT. The polymorphs and morphologies of the CaCO precipitates were tested by using X-ray diffraction and scanning electron microscopy. Further, when Na-MMT was used, the morphology of CaCO changed from an individual precipitate to agglomerations of the precipitate. Compared to the experiments without Na-MMT in the MICP process, the addition of Na-MMT significantly reduced the hydraulic conductivity (HC) of sandy soil consolidated.
Topics: Bentonite; Biotechnology; Calcium Carbonate; Chemical Precipitation; Crystallization; Microscopy, Electron, Scanning; Sand; Soil; Sporosarcina; X-Ray Diffraction
PubMed: 34684789
DOI: 10.3390/molecules26206211 -
Scientific Reports Oct 2021Microbially induced calcium carbonate precipitation (MICP)/Biocementation has emerged as a promising technique for soil engineering applications. There are chiefly two...
Microbially induced calcium carbonate precipitation (MICP)/Biocementation has emerged as a promising technique for soil engineering applications. There are chiefly two methods by which MICP is applied for field applications including biostimulation and bioaugmentation. Although bioaugmentation strategy using efficient ureolytic biocementing culture of Sporosarcina pasteurii is widely practiced, the impact of native ureolytic microbial communities (NUMC) on CaCO mineralisation via S. pasteurii has not been explored. In this paper, we investigated the effect of different concentrations of NUMC on MICP kinetics and biomineral properties in the presence and absence of S. pasteurii. Kinetic analysis showed that the biocementation potential of S. pasteurii is sixfold higher than NUMC and is not significantly impacted even when the concentration of the NUMC is eight times higher. Micrographic results revealed a quick rate of CaCO precipitation by S. pasteurii leading to generation of smaller CaCO crystals (5-40 µm), while slow rate of CaCO precipitation by NUMC led to creation of larger CaCO crystals (35-100 µm). Mineralogical results showed the predominance of calcite phase in both sets. The outcome of current study is crucial for tailor-made applications of MICP.
Topics: Calcium Carbonate; Chemical Precipitation; Crystallization; Kinetics; Microbiota; Sporosarcina
PubMed: 34675302
DOI: 10.1038/s41598-021-00315-5